splitbrain.m

function split = splitbrain(cortex,orientation,b, m)
% Splits the brain and exports a mesh that is a subset of the original
% mesh. Requires the function splitFV (Matlab Exchange)
%
%
% INPUTS:
% cortex - the original mesh. a structure containing tri and vert 
% 
% orientation - slice orientation ('c', 's' or 'a') 'a' is assumed if a
% letter different from 'c' or 's' is used. We always default to coronal
% for simplicity
% 
% slicenum - the slice index on which to cut the mesh. (1-256)
%
% sl - the slope for coronal oblique planes (not configured for 's' or 'a')
%
% OUTPUTS:
% split - a new mesh split at the specified point. A structure containing
% tri and vert
% 
%
%
%     (This is a subfunction created as a part of) Omni-planar and surface
%     casting of epileptiform activity (OPSCEA) (UC Case Number SF2020-281)
%     jointly created by Dr. Jon Kleen, Ben Speidel, Dr. Robert Knowlton,
%     and Dr. Edward Chang is licensed for non-commercial research use at
%     no cost by the Regents of the University of California under CC
%     BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/).
%     Please contact innovation@ucsf.edu if you are interested in using
%     OPSCEA for commercial purposes.

%     The following copyright notice and citation is to be included in any
%     publication, material or media wherein all or a part of Licensed
%     Material is contained, “Certain materials incorporated herein are
%     Copyright © 2016 The Regents of the University of California
%     (REGENTS). All Rights Reserved.

%     Please cite the following paper in your publications if you have used
%     our software in your research, as well as any relevant toolboxes used
%     herein as appropriate (img_pipe, FreeSurfer): Kleen JK, Speidel B,
%     Baud MO, Rao VR, Ammanuel SG, Hamilton LS, Chang EF, Knowlton RC.
%     Accuracy of omni-planar and surface casting of epileptiform activity
%     for intracranial seizure localization. In press at Epilepsia.”


%mind the gap (in mm): prevents triangles tat span the gap from inducing unwanted mesh
thegap = max([abs(5.*m) 5]);
    % NOTE; occasionally produces unwanted side effects for certain
    % slices where a physical gap is inserted between the slice and cortex.
    % Adjusting thegap can help for individual cases but will need a more 
    % unified solution in a future iteration of OPSCEA software.

 if orientation == 'c'
     if (min(cortex.cortex.vert(:,2)) < b) && (b < max(cortex.cortex.vert(:,2)))
           [idx, ~] = sort(find(abs((cortex.cortex.vert(:,2)-(m.*cortex.cortex.vert(:,1) + b + thegap)))<=thegap)); %get indices of verts on slice line
     else; [idx, ~] = sort(find(abs((cortex.cortex.vert(:,2)-(m.*cortex.cortex.vert(:,1) + b + thegap))+2*thegap)<=thegap));
     end
    ph = 1; %counter for the size of the array of tris as it fills
    mesh.tri = cortex.cortex.tri;
    ia22 = zeros(size(idx));
    while(~isempty(intersect(mesh.tri(:,2),idx)))
        [~,ia2,~] = intersect(mesh.tri(:,2),idx); %looks for the tris that match the indices of the verts on the line
        ia22(ph:ph+size(ia2,1)-1) = ia2;
        mesh.tri(ia2,:) = []; %remove the tris from the mesh dataset that have already been counted
        ph = ph+size(ia2,1); %update the counter
    end
    ia22(ph:size(idx)) = [];
    
end

mesh.vert = cortex.cortex.vert;
disp('Generating partial mesh for slice view...')
FVout = splitFV(mesh.tri,mesh.vert);

fv.vert = FVout(1).vertices;
fv.tri = FVout(1).faces;

split = fv;